TX-TL Bootcamp, Jun 2015

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only.

Workshop goals

The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

• Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
• Assemble and test genetic circuits using linear DNA assembly in a single day
• Test and characterize circuits that are part of our current research activities

Summary Schedule

The schedule below gives an overview of the activities during the workshop.

Tue morning 9-11 am: Optional tutorials (details below): Lab basics - meet in 111 Keck	Wed morning 9-11 am: Meet in 111 Keck Analyzing TX-TL results (from overnight run) TX-TL using linear DNA 11 am - 12 pm: set up Golden Gate reactions Group lunch at Chandler (when done)	Thu morning 9:00a - Analyze TX-TL results from previous day [111 Keck] 10:00a - Plan out circuits designs to build and test (with mentors)	Fri morning
Tue afternoon 11 am: Bootcamp starts, 111 Keck (lunch will be provided) Overview of workshop and TX-TL system (Richard) Lab safety briefing (Clare) 1:45-5 pm: SURF check-in and orientation 1:45-3 pm: SURF checkin 1:45-3:45 pm: Housing move in 3:45-5 pm: SURF orientation	Wed afternoon 1:30 - 2:30 pm - SURF safety meeting (mandatory) 2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare) 3:15p - Project discussions (with co-mentors) 4:00p - Run gels to confirm PCR results 4:30p - Continue project discussions 5:30p - Set up FFL runs from GGA assembly	Thu afternoon Set up characterization runs	Fri afternoon Adjourn by 4 pm
Tue evening 5-7 pm: SURF BBQ Lab session: 7-9 pm Set up and run first TX-TL reactions	Wed evening 6:30-8 pm: Group dinner on S. Lake (participants and mentors) Lab session: 8-10 pm Set up TX-TL runs	Thu evening

Description of tutorials:

• Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

• MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

• Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

Read-ahead material

We will assume everyone has watched the following 15 minute video before attending the workshop:

• Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology. Journal. of Visualized Experiments (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:

• J. Shin and V. Noireaux, An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. ACS Synthetic Biology, 1(1):29–41, 2012.

• Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. ACS Synthetic Biology, 2014.

• Biomolecular Breadboards pages on OpenWetWare
  • Modeling overview - setting up simulations using MATLAB-based TX-TL toolbox
  • Preliminary data - includes linear DNA protection, protein degradation
  • More info - additional references and presentations on TX-TL

Software

We will make use of the following software as part of the workshop:

• Microsoft Excel (or Numbers)
• ApE (free), Geneious (free trial)
• MATLAB, Simbiology
• TX-TL modeling toolbox (requires MATLAB 2010+ and SimBiology]

Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.